A custom NPC is different in that instead of having set Skill Points (Except for race bonus), you can assign them yourself! You can hire them inside personal residences or from training academies. To hire an NPC you go inside the facility you want to hire them from, go to the position page, click "Actions", then "Hire NPCs". The rest is easy.

Actually, a custom NPC is typically used for the ability to customise their speech, rather than assigning their skill points. Especially since they can't use those skills for anything at the current time.

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"May the Grace of Ara go with you, and His Vengeance be wrought upon your enemies."

Custom NPCs do not get any pre-set class skills. Instead, they receive some Skill Points (SP) that must be assigned in their skills by the players, using the regular skills rules. Custom class 1 NPC get 5 SP, class 2 get 7 SP, and class 3 get 9 SP.

Custom NPCs can be hired from inside Personal Residence, Training Academy for a base cost of 80,000 credits.”

by semi-working, he means the speak-tree link is bugged and only works part of the time.

Well not this. Also the reason the only available NPC is a resident in your Personal Resident is quite logic. Why would for example a Grenadier or a Rifleman be for hire in your house. You have to go to a Spaceport for Space NPCs, to a Barrack etc. for Military NPCs etc. You can see it on the rules page of each facility.